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In a second test, we randomized the case/control status again and added a simulated variant to the gene CAV2 (protein cavelolin-2, induced during adipocyte differentiation), with between 9-20 variant loci (including the simulated variant).
First, we tested BioBin by adding a simulated variant with 100% penetrance to two genes on chromosome 7 in a case-control sample composed of individuals of European descent (CEU).
A simulated variant was added to two genes, GLI3 and CAV2.
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Importantly, this bond is found in the structures of all simulated variants (wild-type, A370V, and I369F).
The addition of one simulated variant loci added a total of 43 variants (each case is heterozygous and only contributes one variant to bin).
We selected the simulated variant 144 A→G, which presents a k-tuple distance of 0.00390 in relation to the Citrus II viroid genome.
We simulated variant abundances adhering to either a uniform or power-law distribution.
GLI3 has a large number of variants in addition to the simulated variant.
As the added variant had 100% penetrance, each case was assigned as a heterozygote and each control was homozygous referent for the simulated variant.
We added our simulated variant to the gene GLI3 (GLI family zinc finger 3), a large gene associated with polydactyly syndrome [OMIM 174200].
We ran shearwater on the cohort of 500 samples to compute the Bayes factors of each simulated variant.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com